<p>Understanding the mechanisms of brain function and dysfunction is at the core of the neuroscience mission. However, the field’s grasp of causal relationships between brain properties has been hindered by a focus on single modalities that neglects the complex interplay between the features found at different neural scales. Progress in neuroinformatics and the increasing availability of open datasets have helped overcome this limitation by facilitating the contextualization of brain maps against cellular, metabolic and network features. Despite the rapid uptake of data contextualization methods proposing that quantification of spatial similarity between brain maps may shed light on pathways of structure–function coupling, development and disease, their potential pitfalls have received little attention. In the context of neuroimaging research, these limitations include reliance on often small-sample and non-representative reference datasets, repeated use of the same brain maps across studies, and problems with intermodal and interindividual alignment. Applying data contextualization without considering these limitations can lead to circular reasoning, overfitting and correlational overreach, and limits the interpretation of findings to the properties of the source data. Here we provide a Roadmap of practical guidelines operating at the level of study design, analysis pipelines and interpretation of findings to encourage the development of best practices in data contextualization. A more informed use of brain map correlation approaches will improve mechanistic investigations and our understanding of causal relationships between brain properties.</p>